Align MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate GFF774 PGA1_c07880 alpha-glucoside transport system permease protein AglG
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__Phaeo:GFF774 Length = 382 Score = 105 bits (262), Expect = 2e-27 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 4/240 (1%) Query: 42 YVPYIIPKTWTLDNY--IKLFTNSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRI 99 +V +P +TL+NY + + NS+ + F NTL V+ ++ + AY+L+ + Sbjct: 144 FVTATVPPEFTLENYETVLISGNSTDNMAKAFFNTLTVTIPATIIPILVAAFAAYALAWM 203 Query: 100 KFKHRNGFLKLALVLNMFPGFMSMIAVYYILKALNLTQTLTSLVLVYSS-GAALTFYIAK 158 +F R + + L + P +++I + + + + + + ++ G L Y+ + Sbjct: 204 EFPGRALLVAAIVGLLVVPLQLALIPLLKFHNEIGIGKGYIGVWMAHTGFGLPLAIYLLR 263 Query: 159 GFFDTIPYSLDESAMIDGATRKDIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVILG 218 + IP + E+A +DGAT IF++I LPLS P + A+ F+ W D + A V L Sbjct: 264 NYMVGIPRDIIENARVDGATDFLIFVRIILPLSFPALASFAIFQFLWTWNDLLVAMVFLI 323 Query: 219 DATSKYTVAIGLFSMLQADTINNWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278 DAT + TV L NW + + V IA+P+ + F MQKY V G+ GSVK Sbjct: 324 DATGETTVMTKQIVELLGTRGGNWEILATSAFVSIAVPLAVFFA-MQKYLVRGLLAGSVK 382 Score = 26.9 bits (58), Expect = 7e-04 Identities = 11/33 (33%), Positives = 22/33 (66%) Query: 4 KKQLQIGSIYALLILLSFIWLFPIIWVILTSFR 36 +K I ++ ++LL +WLFP + ++++SFR Sbjct: 7 EKPALIWALRLSVVLLVGLWLFPTLGLLVSSFR 39 Lambda K H 0.330 0.142 0.428 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 287 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 278 Length of database: 382 Length adjustment: 28 Effective length of query: 250 Effective length of database: 354 Effective search space: 88500 Effective search space used: 88500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory